Modeling of the Peptide Release during Proteolysis of β-Lactoglobulin by Trypsin with Consideration of Peptide Bond Demasking

Prospects for predicting the fragmentation of polypeptide chains during their enzymatic hydrolysis using proteolysis models are considered. The opening of the protein substrate during proteolysis and the exposure of its internal peptide bonds for a successful enzymatic attack, the so-called demasking process, were taken into account. The two-step proteolysis model was used, including the parameters of demasking and the rate constants of hydrolysis of enzyme-specific peptide bonds. Herein, we have presented an algorithm for calculating the concentrations of intermediate and final peptide fragments depending on the time of hydrolysis or the degree of hydrolysis. The intermediate peptide fragments with two or one internal specific peptide bond were considered. The fragmentation of β-lactoglobulin (β-LG) by trypsin was predicted, and the calculated concentration curves for peptide fragments were compared with the experimental dependences of the concentrations on the degree of hydrolysis. Numerical parameters were proposed that characterize the concentration curves for intermediate and final peptide fragments, and they were used to compare the calculated and experimental dependences. The predicted distribution of the peptide fragments corresponded to the experimental data on the peptide release during the proteolysis of β-LG by trypsin.

Polyaspartic acid, 2-acrylamido-2-Methyl propane sulfonic acid and sodium alginate based biocompatible stimuli responsive polymer gel for controlled release of GHK-Cu peptide for wound healing

Stimuli responsive polymer based on Polyaspartic acid, 2-Acrylamido-2-methylpropane sulfonic acid and sodium alginate (NaAlg) were synthesized using two cross-linkers Ethylene glycol dimethacrylate (EGDMA) and TMPTA (Trimethylolpropane triacrylate). The polymers were standardized and optimized to obtain a polymer with maximum swelling in distilled water, saline, glucose and solutions of varying pH. The synthesized polymer swelled well in distilled water, glucose solution and acidic- alkaline medium. The biocompatibility of the polymer was evaluated for blood compatibility and protein adsorption. The polymer with maximum swelling property was used for peptide release studies. The polymer was further used to study the peptide encapsulation and release efficiency of the polymeric material which was confirmed by FTIR, Scanning Emission Microscope and EDX. The encapsulation efficiency of the polymer for encapsulating (glycyl-l-histidyl-l-lysine-copper) GHK-Cu was observed to be 55.26% and peptide release of 51.84% was observed for Ethylene glycol dimethacrylate based polymer after 24 h whereas for Trimethylolpropane triacrylate based polymer the encapsulation efficiency was observed to be 49.6% and release was 39.01%. The EGDMA based polymer was further examined under in vivo studies in order to evaluate the efficiency of the synthesized polymer. The in vivo studies include wound closure, histopathological analysis, biochemical and toxicity assay. The material has shown promising results for both in vivo and in vitro studies.

Antimicrobial Peptides in the Battle against Orthopedic Implant-Related Infections: A Review

Prevention of orthopedic implant-related infections is a major medical challenge, particularly due to the involvement of biofilm-encased and multidrug-resistant bacteria. Current therapies, based on antibiotic administration, have proven to be insufficient, and infection prevalence may rise due to the dissemination of antibiotic resistance. Antimicrobial peptides (AMPs) have attracted attention as promising substitutes of conventional antibiotics, owing to their broad-spectrum of activity, high efficacy at very low concentrations, and, importantly, low propensity for inducing resistance. The aim of this review is to offer an updated perspective of the development of AMPs-based preventive strategies for orthopedic and dental implant-related infections. In this regard, two major research strategies are herein addressed, namely (i) AMP-releasing systems from titanium-modified surfaces and from bone cements or beads; and (ii) AMP immobilization strategies used to graft AMPs onto titanium or other model surfaces with potential translation as coatings. In overview, releasing strategies have evolved to guarantee higher loadings, prolonged and targeted delivery periods upon infection. In addition, avant-garde self-assembling strategies or polymer brushes allowed higher immobilized peptide surface densities, overcoming bioavailability issues. Future research efforts should focus on the regulatory demands for pre-clinical and clinical validation towards clinical translation.

Adsorption of Recombinant Human β-Defensin 2 and Two Mutants on Mesoporous Silica Nanoparticles and Its Effect against Clavibacter michiganensis subsp. michiganensis

Solanum lycopersicum L. is affected among other pests and diseases, by the actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm), causing important economic losses worldwide. Antimicrobial peptides (AMPs) are amphipathic cationic oligopeptides with which the development of pathogenic microorganisms has been inhibited. Therefore, in this study, we evaluate antimicrobial activity of mesoporous silica nanoparticles (MSN5.4) loaded with human β-defensin-2 (hβD2) and two mutants (TRX-hβD2-M and hβD2-M) against Cmm. hβD2, TRX-hβD2-M and hβD2-M presented a half-maximum inhibitory concentration (IC₅₀) of 3.64, 1.56 and 6.17 μg/mL, respectively. MSNs had average particle sizes of 140 nm (SEM) and a tunable pore diameter of 4.8 up to 5.4 nm (BJH). AMPs were adsorbed more than 99% into MSN and a first release after 24 h was observed. The MSN loaded with the AMPs inhibited the growth of Cmm in solid and liquid media. It was also determined that MSNs protect AMPs from enzymatic degradation when the MSN/AMPs complexes were exposed to a pepsin treatment. An improved AMP performance was registered when it was adsorbed in the mesoporous matrix. The present study could expand the applications of MSNs loaded with AMPs as a biological control and provide new tools for the management of phytopathogenic microorganisms.

A HemK class glutamine-methyltransferase is involved in the termination of translation and essential for iron homeostasis in Arabidopsis

Iron (Fe) transport and utilization are controlled by Fe-dependent transcriptional cascades. Many genes participate in these processes, transcriptionally controlled by Fe-status. Thorough knowledge of the translational check-points is lacking. We identified a non-response to Fe-deficiency1-1 (nrf1-1) mutant of Arabidopsis thaliana, which displayed a hypersensitive phenotype under Fe-deficient conditions. By mapping nrf1-1, we found that the AT3G13440 locus encoding a HemK methyltransferase is responsible for the phenotype. Analyses of ProUBQ10:NRF1^CDS overexpression nrf1-1 lines and a T-DNA insertion mutant nrf1-2, confirmed that loss-of-function of NRF1 results in enhanced Fe-starvation-sensitivity. NRF1 is required for the proper expression of the majority of Fe-deficiency-inducible (FDI) genes. The nrf1 mutants accumulated more polysomes in the roots, due to stalled ribosomes on several transcripts. Ribosome-footprint (RF) mapping revealed that ribosomes are stalled at a stop codon that amplified the stalling of trailing ribosomes. We detected higher RF levels in many FDI transcripts in nrf1-2. Our study demonstrates the requirement of NRF1 for an accurate termination of protein synthesis essential not only for a precise iron homeostasis, but also cellular ion balance. NRF1 is also important for normal growth and development. A check-point that fine-tunes peptide release in plants is uncovered.

Spatial Distribution and Solvent Polarity-Triggered Release of a Polypeptide Incorporated into Invertible Micellar Assemblies

Extracting, stabilizing, or delivering biomacromolecules such as proteins and peptides in organic phases have potential applications in biocatalysis, protein extraction, and food antioxidation. However, most current delivery/stabilization platforms face various limitations such as protein/peptide molecular size, platform stability/reusability, and/or potential damage to the cargos. A potential solution to these problems is micellar self-assemblies from amphiphilic invertible polymers, which have recently been demonstrated to be powerful as molecular hosts to deliver both small molecular drugs and functional polypeptides in the aqueous phase. To better understand the function of biomacromolecules and predict the usefulness of the formed invertible micellar assemblies (IMAs) as biomacromolecular hosts in organic phases, it is critical to characterize the spatial distribution, structure, and dynamics of biomacromolecules in the IMA including those upon release. However, the background signals of the IMAs limit the application of most peptide characterization approaches. In this work, we overcome the technical barriers by using site-directed spin labeling electron paramagnetic resonance to probe the spatial arrangement and release of a model, the hemagglutinin (HA) peptide, in the IMAs formed from two different amphiphilic invertible polymers. By site-specifically probing three residues along the peptide chain, for the first time, we depict the possible spatial distribution of HA within the IMAs. By triggering the disassembly of the IMAs with a thermodynamically good solvent (in this study, acetone), we detailed the stability of IMAs in toluene and the peptide release conditions once the polarity of the medium changes. Our findings are important for the application of peptides/proteins at the polar-nonpolar interface or using this interface to extract or deliver biomacromolecules. Our work also demonstrates the power of SDSL-EPR on probing peptide or micelle dynamics, which can be generalized to understand proteins or other biomacromolecules in micellar polymer assemblies in varied applications.

Carboxylic Terminated Thermo-Responsive Copolymer Hydrogel and Improvement in Peptide Release Profile

To improve the release profile of peptide drugs, thermos-responsive triblock copolymer poly (ε-caprolactone-co-p-dioxanone)-b-poly (ethylene glycol)-b-poly (ε-caprolactone-co-p-dioxanone) (PECP) was prepared and end capped by succinic anhydride to give its carboxylic terminated derivative. Both PCEP block copolymer and its end group modified derivative showed temperature-dependent reversible sol-gel transition in water. The carboxylic end group could significantly decrease the sol-gel transition temperature by nearly 10 °C and strengthen the gel due to enhanced intermolecular force among triblock copolymer chains. Furthermore, compared with the original PECP triblock copolymer, HOOC-PECP-COOH copolymer displayed a retarded and sustained release profile for leuprorelin acetate over one month while effectively avoiding the initial burst. The controlled release was believed to be related to the formation of conjugated copolymer-peptide pair by ionic interaction and enhanced solubility of drug molecules into the hydrophobic domains of the hydrogel. Therefore, carboxyl terminated HOOC-PECP-COOH hydrogel was a promising and well-exhibited sustained release carrier for peptide drugs with the advantage of being able to develop injectable formulation by simple mixing.

Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release

Termination of protein synthesis is triggered by the recognition of a stop codon at the ribosomal A site and is mediated by class I release factors (RFs). Whereas in bacteria, RF1 and RF2 promote termination at UAA/UAG and UAA/UGA stop codons, respectively, eukaryotes only depend on one RF (eRF1) to initiate peptide release at all three stop codons. Based on several structural as well as biochemical studies, interactions between mRNA, tRNA, and rRNA have been proposed to be required for stop codon recognition. In this study, the influence of these interactions was investigated by using chemically modified stop codons. Single functional groups within stop codon nucleotides were substituted to weaken or completely eliminate specific interactions between the respective mRNA and RFs. Our findings provide detailed insight into the recognition mode of bacterial and eukaryotic RFs, thereby revealing the chemical groups of nucleotides that define the identity of stop codons and provide the means to discriminate against noncognate stop codons or UGG sense codons.

Uniformity of Peptide Release Is Maintained by Methylation of Release Factors

Termination of protein synthesis on the ribosome is catalyzed by release factors (RFs), which share a conserved glycine-glycine-glutamine (GGQ) motif. The glutamine residue is methylated in vivo, but a mechanistic understanding of its contribution to hydrolysis is lacking. Here, we show that the modification, apart from increasing the overall rate of termination on all dipeptides, substantially increases the rate of peptide release on a subset of amino acids. In the presence of unmethylated RFs, we measure rates of hydrolysis that are exceptionally slow on proline and glycine residues and approximately two orders of magnitude faster in the presence of the methylated factors. Structures of 70S ribosomes bound to methylated RF1 and RF2 reveal that the glutamine side-chain methylation packs against 23S rRNA nucleotide 2451, stabilizing the GGQ motif and placing the side-chain amide of the glutamine toward tRNA. These data provide a framework for understanding how release factor modifications impact termination.

Ribosome Induces a Closed to Open Conformational Change in Release Factor 1

Bacterial translation termination is triggered when a stop codon arrives at the ribosomal A site. Stop codons are recognized by class I release factors (RF1 and RF2 in Escherichia coli), which bind to the ribosome and catalyze the release of the newly synthesized protein. Crystal structures showed that RF1 and RF2 are in an open conformation when bound to the ribosome but are in a closed conformation when not bound to the ribosome. It is not clear whether only the open form of RF1 and RF2 binds to the ribosome. Alternatively, the closed form of RF1 and RF2 may bind to the ribosome and undergo a conformational change to the open state upon binding. We used transition metal ion fluorescence resonance energy transfer experiments to monitor precisely the conformation of RF1 in the absence and presence of the ribosome. Our results indicate that RF1 undergoes a large conformational change from a closed to an open form upon binding to the ribosome. Our results are consistent with the mechanism, in which high termination fidelity is achieved by linking stop codon recognition by RF1 to the change in conformation from closed to open state.

Activation of TRPM3 by a potent synthetic ligand reveals a role in peptide release

Transient receptor potential (TRP) cation channel subfamily M member 3 (TRPM3), a member of the TRP channel superfamily, was recently identified as a nociceptor channel in the somatosensory system, where it is involved in the detection of noxious heat; however, owing to the lack of potent and selective agonists, little is known about other potential physiological consequences of the opening of TRPM3. Here we identify and characterize a synthetic TRPM3 activator, CIM0216, whose potency and apparent affinity greatly exceeds that of the canonical TRPM3 agonist, pregnenolone sulfate (PS). In particular, a single application of CIM0216 causes opening of both the central calcium-conducting pore and the alternative cation permeation pathway in a membrane-delimited manner. CIM0216 evoked robust calcium influx in TRPM3-expressing somatosensory neurons, and intradermal injection of the compound induced a TRPM3-dependent nocifensive behavior. Moreover, CIM0216 elicited the release of the peptides calcitonin gene-related peptide (CGRP) from sensory nerve terminals and insulin from isolated pancreatic islets in a TRPM3-dependent manner. These experiments identify CIM0216 as a powerful tool for use in investigating the physiological roles of TRPM3, and indicate that TRPM3 activation in sensory nerve endings can contribute to neurogenic inflammation.

Voltage-gated Ca2+ influx and mitochondrial Ca2+ initiate secretion from Aplysia neuroendocrine cells

Neuroendocrine secretion often requires prolonged voltage-gated Ca(2+) entry; however, the ability of Ca(2+) from intracellular stores, such as endoplasmic reticulum or mitochondria, to elicit secretion is less clear. We examined this using the bag cell neurons, which trigger ovulation in Aplysia by releasing egg-laying hormone (ELH) peptide. Secretion from cultured bag cell neurons was observed as an increase in plasma membrane capacitance following Ca(2+) influx evoked by a 5-Hz, 1-min train of depolarizing steps under voltage-clamp. The response was similar for step durations of ≥ 50 ms, but fell off sharply with shorter stimuli. The capacitance change was attenuated by replacing external Ca(2+) with Ba(2+), blocking Ca(2+) channels, buffering intracellular Ca(2+) with EGTA, disrupting synaptic protein recycling, or genetic knock-down of ELH. Regarding intracellular stores, liberating mitochondrial Ca(2+) with the protonophore, carbonyl cyanide-p-trifluoromethoxyphenyl-hydrazone (FCCP), brought about an EGTA-sensitive elevation of capacitance. Conversely, no change was observed to Ca(2+) released from the endoplasmic reticulum or acidic stores. Prior exposure to FCCP lessened the train-induced capacitance increase, suggesting overlap in the pool of releasable vesicles. Employing GTP-γ-S to interfere with endocytosis delayed recovery (presumed membrane retrieval) of the capacitance change following FCCP, but not the train. Finally, secretion was correlated with reproductive behavior, in that neurons isolated from animals engaged in egg-laying presented a greater train-induced capacitance elevation vs quiescent animals. The bag cell neuron capacitance increase is consistent with peptide secretion requiring high Ca(2+), either from influx or stores, and may reflect the all-or-none nature of reproduction.

Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA

The last step in ribosome-catalyzed protein synthesis is the hydrolytic release of the newly formed polypeptide from the P-site bound tRNA. Hydrolysis of the ester link of the peptidyl-tRNA is stimulated normally by the binding of release factors (RFs). However, an unacylated tRNA or just CCA binding to the ribosomal A site can also stimulate deacylation under some nonphysiological conditions. Although the sequence of events is well described by biochemical studies, the structural basis of the mechanism underlying this process is not well understood. Two new structures of the large ribosomal subunit of Haloarcula marismortui complexed with a peptidyl-tRNA analog in the P site and two oligonucleotide mimics of unacylated tRNA, CCA and CA, in the A site show that the binding of either CA or CCA induces a very similar conformational change in the peptidyl-transferase center as induced by aminoacyl-CCA. However, only CCA positions a water molecule appropriately to attack the carbonyl carbon of the peptidyl-tRNA and stabilizes the proper orientation of the ester link for hydrolysis. We, thus, conclude that both the ability of the O3'-hydroxyl group of the A-site A76 to position the water and the A-site CCA induced conformational change of the PTC are critical for the catalysis of the deacylation of the peptidyl-tRNA by CCA, and perhaps, an analogous mechanism is used by RFs.

Modulating the activity of the peptidyl transferase center of the ribosome

The peptidyl transferase (PT) center of the ribosome catalyzes two nucleophilic reactions, peptide bond formation between aminoacylated tRNA substrates and, together with release factor, peptide release. Structure and function of the PT center are modulated by binding of aminoacyl-tRNA or release factor, thus providing the basis for the specificity of catalysis. Another way by which the function of the PT center is controlled is signaling from the peptide exit tunnel. The SecM nascent peptide induces ribosome stalling, presumably by inhibition of peptide bond formation. Similarly, the release factor-induced hydrolytic activity of the PT center can be suppressed by the TnaC nascent peptide contained in the exit tunnel. Thus, local and long-range conformational rearrangements can lead to changes in the reaction specificity and catalytic activity of the PT center.

Costorage and corelease of modulatory peptide cotransmitters with partially antagonistic actions on the accessory radula closer muscle of Aplysia californica

Many neurons that contain a classical neurotransmitter also contain modulatory peptides, but it has been difficult to establish unequivocally that these peptides are functional cotransmitters. Here, we provide evidence for functional cotransmission in a neuromuscular system of Aplysia. Using immunocytochemical techniques, we localize members of two peptide families, the small cardioactive peptides (SCPs) and the buccalins (BUCs), to a single subset of dense-core vesicles in the terminals of the cholinergic motorneuron B15. We describe a new preparation and method for the direct detection of released peptides and show that the SCPs and BUCs are released when neuron B15 is intracellularly stimulated. Consistent with their subcellular localization, the SCPs and BUCs are released in a stoichiometric ratio that is constant across conditions that change the absolute amount of peptides released. Peptide release is calcium-dependent but does not require muscle contractions. Thus, the release cannot be attributed to a displacement of peptides that may be present in the extracellular space. In previous studies, we characterized the physiological firing patterns of neuron B15. Here, we simulate these firing patterns and show that peptide release occurs. Additionally, we find that significant quantities of material are released under behaviorally relevant conditions. We find that concentrations of released peptides in the muscle are in the concentration range in which exogenously applied peptides exert characterized modulatory actions on muscle contractions. Together, our findings provide strong support for the hypothesis that peptides contained in neuron B15 are functional cotransmitters.

Release of peptide cotransmitters in Aplysia: regulation and functional implications

To gain insights into the physiological role of cotransmission, we measured peptide release from cell B15, a motorneuron that utilizes ACh as its primary transmitter but also contains putative peptide cotransmitters, the small cardioactive peptides (SCPs) and the buccalins (BUCs). All stimulation parameters used were in the range in which B15 fires in freely moving animals. We stimulated neuron B15 in bursts and systematically varied the interburst interval, the intraburst frequency, and burst duration. Both peptides were preferentially released when B15 was stimulated at higher intra- or interburst frequencies or with longer burst durations. Across stimulation patterns, the amount of peptide released depended on the mean frequency of stimulation and was independent of the specific pattern of stimulation. The parameters of stimulation that produce a larger release of peptides correspond to those that evoke larger contractions. Large and frequent contractions are likely to fuse or summate, thus disrupting the rhythmic behavior mediated by the muscle innervated by motorneuron B15. Because the combined effect of the SCPs and BUCs is to accelerate the relaxation and shorten the duration of muscle contractions, these peptides reduce the probability of the disruptive fusion or summation of muscle contractions. Because these cotransmitters regulate an aspect of muscle contractions that is not controlled by acetylcholine (ACh), the primary transmitter of B15, we suggest that peptides and ACh form parallel but functionally distinct lines of transmission at the neuromuscular junction. Both types of transmission may be necessary to ensure that behavior remains efficient over a wide range of conditions.